flonat-research 0.1.0

package/skills/init-project-course/references/memory-and-settings.md

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+# Phase 5-7: MEMORY.md Templates, Settings & Vault Sync
+
+> Templates for seeding MEMORY.md, settings.local.json, and vault pipeline sync for `/init-project-course`.
+
+---
+
+## MEMORY.md — Student Module Template
+
+```markdown
+# MEMORY — [Module Code] [Module Name]
+
+## Notation Registry
+
+| Variable | Convention | Anti-pattern |
+|----------|-----------|--------------|
+
+## Key Decisions
+
+| Decision | Rationale | Date |
+|----------|-----------|------|
+
+## Code Pitfalls
+
+| Bug | Impact | Fix |
+|-----|--------|-----|
+```
+
+## MEMORY.md — Instructor Module Template
+
+```markdown
+# MEMORY — [Module Code] [Module Name]
+
+## Student Misconceptions
+
+| Misconception | Correction | How to address |
+|---------------|-----------|----------------|
+
+## Marking Notes
+
+| Pattern | Frequency | Comment |
+|---------|-----------|---------|
+
+## Code Pitfalls
+
+| Bug | Impact | Fix |
+|-----|--------|-----|
+```
+
+---
+
+## Settings — settings.local.json
+
+If `.claude/settings.local.json` exists, leave it. If not, create one:
+
+```json
+{
+  "permissions": {
+    "allow": [
+      "Bash(latexmk *)",
+      "Bash(ls:*)",
+      "Bash(mkdir:*)",
+      "Bash(tree:*)",
+      "Bash(npm *)",
+      "Bash(node *)",
+      "Edit",
+      "Glob",
+      "Grep",
+      "Read",
+      "Write"
+    ],
+    "deny": []
+  }
+}
+```
+
+---
+
+## vault pipeline Sync
+
+Offer to create a row in the appropriate vault pipeline. If the user accepts:
+
+### Student module → Modules Pipeline (Student)
+
+- **Database data source ID:** `YOUR-MODULES-STUDENT-DATABASE-ID-HERE`
+- Set: Module Name, Module Code, University, Programme, Term, Year, Status, Assessment Type, Credits, Instructor, Folder Path, Has CLAUDE.md = `__YES__`
+
+### Instructor module → Modules Pipeline (Instructor)
+
+- **Database data source ID:** `YOUR-MODULES-INSTRUCTOR-DATABASE-ID-HERE`
+- Set: Module Name, Module Code, University, Term, Year, Role, Status, Module Leader, Folder Path, Has CLAUDE.md = `__YES__`
+
+Use information gathered from the interview. Leave unknown fields empty rather than guessing.

package/skills/init-project-course/references/organise-templates.md

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+# Phase 3: Organise — Templates & Handling Rules
+
+> Directory structure templates, workshop naming, and file handling rules for `/init-project-course` Phase 3.
+
+---
+
+## Student Template
+
+For modules where the user is a student:
+
+```
+module-folder/
+├── lectures/ or seminars/   # Lecture slides or seminar papers/readings
+├── notes/                   # Personal notes, reading summaries
+├── recordings/              # Lecture recordings (if any video files exist)
+├── workshops/
+│   ├── 01-topic-slug/
+│   ├── 02-topic-slug/
+│   └── ...
+├── assessments/
+│   ├── group-work/          # Only if group assessment exists
+│   ├── individual/          # Only if individual assessment exists
+│   └── exam/                # Only if exam exists
+├── docs/                    # Module specification, guidelines, syllabi
+├── reviews/                 # Created on demand by review agents
+├── to-sort/                 # Inbox for unsorted files
+├── .claude/
+│   └── settings.local.json
+├── CLAUDE.md
+└── MEMORY.md                # Notation registry, code pitfalls (seeded)
+```
+
+**Use `seminars/` instead of `lectures/`** when the module is discussion-based (no traditional lectures — e.g., IB9PK-style with seminar papers and readings).
+
+## Instructor Template
+
+For modules where the user teaches:
+
+```
+module-folder/
+├── lectures/ or classes/    # Lecture slides
+├── recordings/              # Lecture recordings (if any video files exist)
+├── workshops/ or labs/
+│   ├── 01-topic-slug/
+│   ├── 02-topic-slug/
+│   └── ...
+├── assessments/
+│   ├── group-work/          # Only if group assessment exists
+│   ├── individual/          # Only if individual assessment exists
+│   └── exam/                # Only if exam exists
+├── marking/                 # Marking scripts, rubrics, feedback templates
+├── shared-folder/           # Student-facing materials (if applicable)
+├── docs/                    # Module specification, guidelines
+├── reviews/                 # Created on demand by review agents
+├── to-sort/                 # Inbox for unsorted files
+├── .claude/
+│   └── settings.local.json
+├── CLAUDE.md
+└── MEMORY.md                # Student misconceptions, code pitfalls (seeded)
+```
+
+## Workshop Naming
+
+- Format: `XX-topic-slug/` (zero-padded number + kebab-case topic)
+- Infer topic from folder name if descriptive (e.g., "Workshop 1 - JavaScript Bootcamp" → `01-javascript-bootcamp`)
+- For ambiguous names (e.g., "Workshop 6" with no description), try to identify the topic:
+  - Read any PDF or `.docx` inside the folder
+  - Check file names for clues
+  - If still unclear, **ask the user** for that specific workshop
+- Preserve numbering gaps — do NOT renumber (Week 11 stays `11-`, not `07-`)
+
+## Lecture PDF Handling
+
+- Collect ALL lecture PDFs into `lectures/` (or `seminars/`) from wherever they are scattered (root, workshop folders, assessment folders)
+- **Deduplicate** — if the same filename appears in multiple locations, keep one copy in `lectures/` and remove the rest
+- Do NOT rename lecture PDFs — keep original filenames
+- Workshop-specific PDFs (exercise sheets, briefs) stay in their workshop folder
+
+## Recording Handling
+
+- Only create `recordings/` if video files are detected in the scan
+- Move all lecture recordings to `recordings/`
+- If recordings are already in a sensibly named folder, rename to `recordings/` rather than creating a new one
+
+## Assessment Handling
+
+- Only create subcategories under `assessments/` that the user confirmed exist
+- Never guess assessment types — if unclear, ask
+
+## Rules
+
+- Present the full move plan as a list before executing
+- Never move files without explicit approval
+- If the existing structure is already clean, say so and only suggest minor fixes

package/skills/init-project-course/skill.md

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+---
+name: init-project-course
+description: "Use when you need to bootstrap a university course or module folder."
+allowed-tools: Bash(mkdir*), Bash(mv*), Bash(ls*), Bash(tree*), Bash(find*), Bash(rm*), Bash(cp*), Read, Write, Edit, Glob, Grep, AskUserQuestion
+argument-hint: "[no arguments — runs in current directory]"
+---
+
+# Init Project Course
+
+> Bootstrap a university course or module folder into a clean, navigable structure. Designed for taught modules with lectures, workshops, assessments, and optionally recordings.
+
+## When to Use
+
+- University modules with lectures + workshops + assessments
+- Course folders that have accumulated files over a term
+- When the user says "organise this module", "init course", "set up this module folder"
+- Any taught course with recurring weekly components
+
+## When NOT to Use — Escalate
+
+- To `/init-project-light` if it's a one-off document collection (no lectures/workshops structure)
+- To `/init-project-research` if it's a research project that happens to be for a course
+
+---
+
+## Phase 1: Scan
+
+Read everything already in the directory before asking questions.
+
+1. List all files and folders (excluding `.claude/`, `.DS_Store`)
+2. Identify content types:
+   - **Lecture PDFs** — files matching `Lecture*` or containing "lecture" in name
+   - **Seminar materials** — files matching `Seminar*`, `Session*`, or containing "seminar" in name (discussion-based modules use seminars instead of lectures)
+   - **Lecture recordings** — video files (`.mp4`, `.mov`, `.mkv`, `.webm`, `.avi`) or folders named `recordings`
+   - **Workshop folders** — folders matching `Workshop*`, `Lab*`, `Week*`, or numbered folders with exercise content
+   - **Assessment folders** — folders containing "group", "individual", "exam", "coursework", "assignment", "portfolio"
+   - **Workshop PDFs** — PDFs inside workshop folders that are NOT lectures (exercise sheets, briefs)
+   - **Code projects** — `node_modules/`, `package.json`, `.py`, `.js`, `.ts` files inside workshop folders
+   - **Notes** — personal notes, reading lists, exercise solutions (common in student modules)
+3. Detect duplicates: lecture PDFs that appear in multiple locations
+4. Note workshop numbering gaps (normal — not every week has a workshop)
+5. Check for existing organisation (already has `lectures/`, `workshops/`, etc.)
+
+**Goal:** Build a complete inventory so the interview is short.
+
+---
+
+## Phase 2: Interview (4-5 questions max)
+
+Use `AskUserQuestion`. Only ask what you couldn't infer from Phase 1.
+
+Pick from these (skip any you can already answer):
+
+1. **What module is this?** — code + name (e.g., "IB9PK Advances in Behavioural Science")
+2. **Are you a student or instructor?** — determines template variant (see Phase 3)
+3. **Who teaches it?** — name(s) and role(s) (for student modules: instructor name; for instructor modules: module leader if different)
+4. **What components exist?** — lectures/seminars, workshops, group work, individual work, exams, recordings
+5. **Status?** — still in progress (more content coming) or archived/complete
+
+If Phase 1 gave you enough, confirm your understanding instead of asking:
+> "This looks like [module code + name]. You're [student/instructor]. It has [N] workshops, [N] lecture PDFs, and [assessment types]. Still in progress. Correct?"
+
+**Always interview** — even if scan is comprehensive. Course folders affect a full term of work; assumptions are expensive.
+
+---
+
+## Phase 3: Organise
+
+Present the proposed structure and **wait for explicit approval** before moving anything.
+
+Full templates (student + instructor directory structures), workshop naming, lecture/recording/assessment handling rules: [references/organise-templates.md](references/organise-templates.md)
+
+---
+
+## Phase 4: Create CLAUDE.md
+
+Follow the `lean-claude-md` rule. Include only:
+
+1. **Module overview** — code, name, institution, programme, credits, 1-2 sentence description
+2. **People** — instructor(s) and/or student, role
+3. **Assessment** — type(s), format, word count/page limit, deadline(s) if known
+4. **Directory structure** — compact tree of the organised layout
+5. **Conventions** — detectable patterns (LaTeX compilation, GitHub repo naming, submission format)
+6. **Status note** — "in progress" or "complete/archived", with note on what's still to come
+
+**Do NOT include:**
+- Lecture-by-lecture notes
+- Workshop solution details
+- Full assessment criteria (those live in `docs/` or `assessments/`)
+- Anything that duplicates global rules
+
+---
+
+## Phase 5: Seed MEMORY.md
+
+Create `MEMORY.md` using the appropriate template (student or instructor). Templates, settings.local.json, and vault pipeline sync details: [references/memory-and-settings.md](references/memory-and-settings.md)
+
+---
+
+## Phase 6: Settings
+
+Create `.claude/settings.local.json` if missing. Full details: [references/memory-and-settings.md](references/memory-and-settings.md)
+
+---
+
+## Phase 7: vault pipeline Sync
+
+Offer to create a row in the appropriate Modules Pipeline (Student or Instructor). Database IDs and field mappings: [references/memory-and-settings.md](references/memory-and-settings.md)
+
+---
+
+## Phase 8: Confirmation
+
+Short report:
+
+```
+Set up course project: <module code + name>
+Role: Student / Instructor
+
+Created:
+  - CLAUDE.md
+  - MEMORY.md (seeded with [student/instructor] template)
+  - lectures/ or seminars/ (N PDFs, deduplicated from M locations)
+  - notes/ (student only, if applicable)
+  - recordings/ (if applicable)
+  - workshops/ (N workshops, renamed from original folders)
+  - assessments/{types}/ (moved from original folders)
+  - docs/ (module specification, guidelines)
+  - [.claude/settings.local.json if created]
+  - [vault entry created in Modules Pipeline (Student/Instructor)]
+
+Workshop naming:
+  "Workshop 1 - JavaScript Bootcamp" → workshops/01-javascript-bootcamp
+  "Workshop 6" → workshops/06-cwe-vulnerability-analysis
+  ...
+```
+
+---
+
+## Cross-References
+
+| Skill | Relationship |
+|-------|-------------|
+| `/init-project-light` | For non-course document collections |
+| `/init-project-research` | For research projects within a course |
+| `/audit-project-course` | Run later to check the structure is still clean |
+| `/update-project-doc` | Run later to refresh CLAUDE.md if the module grows |

package/skills/init-project-light/skill.md

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+---
+name: init-project-light
+description: "Use when you need to bootstrap a lightweight project with minimal structure."
+allowed-tools: Bash(mkdir*), Bash(ls*), Bash(touch*), Read, Write, Edit, Glob, Grep, AskUserQuestion
+argument-hint: "[no arguments — runs in current directory]"
+---
+
+# Init Project Light
+
+> Lightweight project bootstrapper for small projects that don't need the full `/init-project-research` scaffold.
+
+## When to Use
+
+- Small document collections (proposals, applications, meeting notes)
+- One-off or short-lived projects
+- Projects without a code pipeline or Overleaf link
+- When the user says "set up something light", "quick init", "organise this folder"
+- Any project that doesn't warrant `/init-project-research`
+
+## When NOT to Use — Escalate to `/init-project-research`
+
+- Research papers targeting a journal or conference
+- Projects with code, data, or computational pipelines
+- Anything that needs Overleaf, git, or a vault pipeline entry
+
+---
+
+## Phase 1: Scan
+
+Read everything already in the directory before asking questions.
+
+1. List all files and folders (excluding `.claude/`, `.DS_Store`)
+2. Read text files (`.md`, `.tex`, `.bib`, `.txt`) to understand content — respect file size (skip files > 500 lines, note them)
+3. Build a mental model: what is this project, what's the main output, who's involved?
+
+**Goal:** Minimise interview questions by inferring answers from existing files.
+
+---
+
+## Phase 2: Interview (2-3 questions max)
+
+Use `AskUserQuestion`. Only ask what you couldn't infer from Phase 1.
+
+Pick from these (skip any you can already answer):
+
+1. **What is this project?** — one sentence (e.g., "PhD research proposal for [University]")
+2. **What's the main output?** — document, application, collection of notes, etc.
+3. **Anyone else involved?** — names and roles if relevant
+
+If Phase 1 gave you enough, confirm your understanding instead of asking:
+> "From the files, this looks like [X]. The main output is [Y]. Correct?"
+
+---
+
+## Phase 3: Create CLAUDE.md
+
+Follow the `lean-claude-md` rule. Include only:
+
+1. **Project overview** — 2-3 sentences from interview/scan
+2. **People** — if collaborators/supervisors exist
+3. **Directory structure** — compact tree of what exists
+4. **Conventions** — only if detectable (e.g., LaTeX compilation, bibliography style)
+5. **Key context** — anything a future session needs to know immediately
+
+**Do NOT include:**
+- Detailed literature notes or reference lists
+- Action items or timelines (those go to vault)
+- Anything that duplicates global rules
+
+---
+
+## Phase 4: Organise (suggest, don't force)
+
+Based on what's in the directory, **suggest** lightweight organisation. Present options and wait for approval.
+
+### Standard suggestions
+
+| Folder | When to suggest |
+|--------|----------------|
+| `to-sort/` | Multiple unsorted documents exist |
+| `docs/` | Reference materials, guidelines, or background reading present |
+| `archive/` | Old versions or abandoned drafts detected |
+
+### Rules
+
+- Never create more than 2-3 folders — this is a light project
+- Never move files without explicit approval
+- If the existing structure already makes sense, say so and skip this phase
+- If there's a `.claude/settings.local.json`, leave it. If not, create one with standard permissions.
+
+### Standard permissions (`.claude/settings.local.json`)
+
+```json
+{
+  "permissions": {
+    "allow": [
+      "Bash(latexmk *)",
+      "Bash(ls:*)",
+      "Bash(mkdir:*)",
+      "Bash(tree:*)",
+      "Edit",
+      "Glob",
+      "Grep",
+      "Read",
+      "Write"
+    ],
+    "deny": []
+  }
+}
+```
+
+Only create if missing. Never overwrite existing permissions.
+
+---
+
+## Phase 5: Confirmation
+
+Short report:
+
+```
+Set up lightweight project: <name>
+
+Created:
+  - CLAUDE.md
+  - [any folders created]
+  - [.claude/settings.local.json if created]
+
+Skipped (use /init-project-research if needed later):
+  - Git, Overleaf, vault pipeline, code scaffold
+```
+
+---
+
+## Cross-References
+
+| Skill | Relationship |
+|-------|-------------|
+| `/init-project-research` | Escalate to this for full research projects |
+| `/update-project-doc` | Run later to refresh CLAUDE.md if the project grows |